For Hashmalum
Sorry for the vague-ness of the statement. What I should have said was:
In the case of a spell where hearing the command (i.e. almost any charm-type spell) a silence spell would defend because you can't hear the command (unless the user of the charm were telepathic, then you're in trouble). As well, any spell where the sound-waves (which have no noise) are the carrier of the effect, then they would affect the area within silence.
As an example for the sound-wave attack, we'll take the sonic substituted Fireball. Now then, there are two possible ideas here.
1) The DM rules that the causer of damage comes from the sound. Effectively, the pure loudness (is that even a word?

) causes the pain and damage. If this is the case, then silence would protect.
2) The damage is actually caused by the sound-waves. Essentially, the sonic boom buffets the affected people and causes damage. As well, rocks and such thrown by the pure force of the sound-waves hurt the people, explaining the damage.
This is just my interpretation of the situation. As well, for the sonic sub'ed fireball, I would likely choose option number two. It follows with house rules I used in 2e for fireballs and makes my DM-ing life easier.